[gmx-users] EM error

[Xu Dong Huang]

@ Justin,

Thank you, that worked like a charm!  (Using increased vanderwal distance)

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 9, 2013, at 8:42 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:

> Everytime I remove the atom that is causing the INF force, it gives me new atom that causes INF force. (The ones that come up are all water beads that are causing the infinite force), does that mean when i did genbox it inserted water incorrectly? (Because I viewed it in VMD< it's certainly not overlapping with my solute. )
> 
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudongh at eden.rutgers.edu 
> 
> On Jan 9, 2013, at 8:12 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
> 
>> Dear users,
>> 
>> Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: 
>> 
>> Steepest Descents:
>>  Tolerance (Fmax)   =  1.00000e+01
>>  Number of steps    =        50000
>> Step=   14, Dmax= 1.2e-06 nm, Epot=  4.48322e+19 Fmax=         inf, atom= 14524
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>> 
>> Double precision normally gives you higher accuracy.
>> 
>> writing lowest energy coordinates.
>> 
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  =  4.4832208e+19
>> Maximum force     =            inf on atom 14524
>> Norm of force     =            inf
>> 
>> gcq#182: "That Was Cool" (Beavis and Butthead)
>> 
>> -----My EM.mdp file contains the following: 
>> integrator               = steep
>> dt                       = 0.020
>> nsteps                   = 50000 ;Note: 100 steps is to much for a vacuum run (nsteps=10)
>> 
>> nstlog                   = 1000
>> nstenergy                = 500
>> nstxtcout                = 500
>> 
>> nstlist                  = 10
>> ns_type                  = grid
>> pbc                      = xyz
>> periodic_molecules       = no
>> rlist                    = 1.4
>> 
>> coulombtype              = Shift
>> rcoulomb_switch          = 0.0
>> rcoulomb                 = 1.2
>> epsilon_r                = 15
>> epsilon_rf               = 1
>> vdw_type                 = Shift
>> rvdw_switch              = 0.9
>> rvdw                     = 1.2
>> 
>> My system size 73191 W, and 1 star (consisted of 101 atoms)
>> I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big 
>> 
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering 
>> xudongh at eden.rutgers.edu 
>> 
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